polish_freq: Polishing compared frequencies.
In jtmccr1/HIVEr: Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort
Description
Usage
Arguments
Value
Examples
Description
This function polishes a frequency comparision data frame. The output
is a subset of the initial data frame only containing loci that are
polymorphic in the specified sample.This function is needed because there are cases where a major allele
exists but there is not minor allele because of sequencing errors. In much of the analysis
we are only interested in polymophisms. This function ensures that is all we observe.
Usage
1
polish_freq(df, relative, min_freq = 0)
Arguments
df
data frame with columns freq1 and freq2
relative
either freq1 or freq2 . unquoted. only look at sites with frequency above 0 at freq1,freq2
min_freq
the minumun frequency allowed. frequencies below will be set to 0. those above to 1
Value
a data frame with polymophoric loci
Examples
1
2
get_freqs(c("HS1595","HS1563"),small_isnv)->small_dups
polish_freq(small_dups,freq1,0.02)
jtmccr1/HIVEr documentation built on May 29, 2019, 1:50 a.m.
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Description Usage Arguments Value Examples
Description
This function polishes a frequency comparision data frame. The output is a subset of the initial data frame only containing loci that are polymorphic in the specified sample.This function is needed because there are cases where a major allele exists but there is not minor allele because of sequencing errors. In much of the analysis we are only interested in polymophisms. This function ensures that is all we observe.
Usage
1 | polish_freq(df, relative, min_freq = 0)
|
Arguments
df |
data frame with columns freq1 and freq2 |
relative |
either freq1 or freq2 . unquoted. only look at sites with frequency above 0 at freq1,freq2 |
min_freq |
the minumun frequency allowed. frequencies below will be set to 0. those above to 1 |
Value
a data frame with polymophoric loci
Examples
1 2 | get_freqs(c("HS1595","HS1563"),small_isnv)->small_dups
polish_freq(small_dups,freq1,0.02)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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